LalnView is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments.
The program is also able to display sequence features (active site, domain, motif, propeptide, exon, intron, promoter, etc.) along with the alignment. This allows one to make the link between sequence similarity and known functions.
Lalnview was developped by Lauret Duret and Jean-Francois Gout.
When using LalnView through these servers, sequence features are automatically extracted from database annotations and displayed with the alignment. A screen shot of the main window is available here. Full text sequences are displayed in a secondary window (see the screen shoot). By clicking on a block, the user can visualize the corresponding local alignment. As domain can be repeated in a sequence, iterative clicking on one block will successively display all the similar blocks that occur in the other sequence. For more details, please read the documentation.
You will find some example data file here and the on-line help file.
Other platforms: LalnView source code (C++) is available here (under the GNU GPL licence). In principle, it should be possible to compile LalnView on any platform. Note however that the source code has been tested only for the platforms mentioned above.
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